Comprehensive Hearing Loss and Deafness Panel

Updated
Summary
  • Is a 202 gene panel that includes assessment of non-coding variants
  • Is ideal for patients with a clinical suspicion of syndromic or non-syndromic genetic hearing loss.

Analysis methods
  • PLUS
Availability

4 weeks

Number of genes

202

Test code

EA0501

Panel size

Large

CPT codes
81430

Summary

The Blueprint Genetics Comprehensive Hearing Loss and Deafness Panel (test code EA0501):

ICD codes

Commonly used ICD-10 code(s) when ordering the Comprehensive Hearing Loss and Deafness Panel

ICD-10 Disease
E70.30 Waardenburg syndrome
Q87.89 Alport syndrome
H90.5 Sensorineural hearing loss, unilateral and bilateral
E07.1 Pendred syndrome
H35.50 Usher syndrome, type IV
Q89.8 Stickler syndrome
G31.89 Mohr-Tranebjaerg syndrome
H35.50 Norrie disease
Q75.4 Treacher Collins syndrome
Q89.8 CHARGE syndrome
Q87.89 Branchio-oto-renal (BOR) syndrome

Sample Requirements

  • Blood (min. 1ml) in an EDTA tube
  • Extracted DNA, min. 2 μg in TE buffer or equivalent
  • Saliva (Oragene DNA OG-500 kit/OGD-500 or OG-575 & OGD-575)

Label the sample tube with your patient's name, date of birth and the date of sample collection.

Note that we do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue. Read more about our sample requirements here.

Subpanel description

This comprehensive panel includes genes from the following panels: Alport Syndrome Panel, Branchio-Oto-Renal (BOR) Syndrome Panel, Non-Syndromic Hearing Loss Panel, Pendred Syndrome Panel, Stickler Syndrome Panel, Syndromic Hearing Loss Panel, Usher Syndrome Panel and Waardenburg Syndrome Panel.

Hearing loss is a genetically very heterogenous group of phenotypes varying in severity and causes. Non-syndromic sensorineural hearing loss is a partial or total loss of hearing that occurs without other associated clinical findings. In syndromic hearing loss, symptoms affecting other parts of the body occur in addition to hearing impairment or deafness. Sensorineural hearing loss can be unilateral or bilateral and it can be stable or progressive. In addition, the loss may appear with various intensivity to high, middle or low tones. It is estimated that approximately 60-80% of congenital hearing loss is genetic in origin. Some 60%-to-70% of congenital hereditary hearing impairnment have a non-syndromic origin. The prevalence of non-syndromic hearing loss is 3-4:10,000 neonates and increases with age. In many populations, mutations in GJB2 are the most prevalent explaining up to 50% of all non-syndromic hearing losses. Altogether syndromic hearing loss accounts for 20% to 30% of congenital hearing loss and deafness and the combined prevalence of syndromic hearing loss is approximately 1-2:10,000.

Genes in the Comprehensive Hearing Loss and Deafness Panel and their clinical significance

Gene Associated phenotypes Inheritance ClinVar HGMD
ABHD12 Polyneuropathy, hearing loss, ataxia, retinitis pigmentosa, and cataract AR 16 20
ACTG1* Deafness, Baraitser-Winter syndrome AD 27 47
ADCY1 Deafness AR 1 1
ADGRV1 Usher syndrome, type IV, Febrile seizures, familial, 4 AR 71 236
AIFM1 Deafness, Combined oxidative phosphorylation deficiency 6, Cowchock syndrome XL 27 31
ALMS1* Alström syndrome AR 197 302
ANKH Calcium pyrophosphate deposition disease (familial chondrocalcinosis type 2), Craniometaphyseal dysplasia autosomal dominant type AD 13 20
ARSG Usher syndrome, type IV AR 1 1
ATP2B2 Sensorineural hearing loss AD 3 7
ATP6V1B1 Renal tubular acidosis with deafness AR 15 56
ATP6V1B2 Deafness, congenital, with onychodystrophy, autosomal dominant, Zimmermann-Laband syndrome 2 AD 6 3
BCS1L Bjornstad syndrome, GRACILE syndrome, Leigh syndrome, Mitochondrial complex III deficiency, nuclear type 1 AR 42 37
BDP1* Hearing loss AD/AR 1 1
BSND Sensorineural deafness with mild renal dysfunction, Bartter syndrome AR 10 20
BTD Biotinidase deficiency AR 170 247
C10ORF2 Perrault syndrome, Mitochondrial DNA depletion syndrome, Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant, 3 AR 37 80
CABP2 Deafness AR 1 6
CACNA1D Primary aldosteronism, seizures, and neurologic abnormalities, Sinoatrial node dysfunction and deafness AD/AR 7 8
CATSPER2* Male Infertility, Deafness AR 2 7
CCDC50 Deafness AD 1 4
CD151 Raph blood group, Nephropathy with pretibial epidermolysis bullosa and deafness AR 1 3
CD164 Deafness, autosomal dominant 66 AD 1 1
CDC14A Deafness, autosomal recessive 105 AR 7 9
CDC42* Takenouchi-Kosaki syndrome, Noonan-syndrome like phenotype AD 11 9
CDH23 Deafness, Usher syndrome, type IV AR/Digenic 94 358
CDK9 AR 1
CDKN1C Beckwith-Wiedemann syndrome, IMAGE syndrome AD 35 81
CEACAM16 Deafness AD/AR 4 4
CEP250 Cone rod dystrophy and hearing loss AR 5
CEP78 Cone rod dystrophy and hearing loss AR 7 9
CHD7 Isolated gonadotropin-releasing hormone deficiency, CHARGE syndrome AD 276 860
CHSY1 Temtamy preaxial brachydactyly syndrome AR 6 16
CIB2 Deafness, Usher syndrome, type IV AR 5 18
CLDN14 Deafness AR 11 12
CLIC5 Deafness AR 1 2
CLPP Deafness AR 4 13
CLRN1 Retinitis pigmentosa, Usher syndrome, type IV AR 24 39
COCH Deafness AD 14 29
COL11A1 Marshall syndrome, Fibrochondrogenesis, Stickler syndrome type 2 AD/AR 34 94
COL11A2 Weissenbacher-Zweymuller syndrome, Deafness, Otospondylomegaepiphyseal dysplasia, Fibrochondrogenesis, Stickler syndrome type 3 (non-ocular) AD/AR 29 57
COL2A1 Avascular necrosis of femoral head, Rhegmatogenous retinal detachment, Epiphyseal dysplasia, with myopia and deafness, Czech dysplasia, Achondrogenesis type 2, Platyspondylic dysplasia Torrance type, Hypochondrogenesis, Spondyloepiphyseal dysplasia congenital (SEDC), Spondyloepimetaphyseal dysplasia (SEMD) Strudwick type, Kniest dysplasia, Spondyloperipheral dysplasia, Mild SED with premature onset arthrosis, SED with metatarsal shortening, Stickler syndrome type 1 AD 180 561
COL4A3 Alport syndrome, Hematuria, benign familial AD/AR 123 264
COL4A4 Alport syndrome AD/AR 110 232
COL4A5 Alport syndrome XL 704 992
COL4A6 Deafness, with cochlear malformation XL 11 5
COL9A1 Stickler syndrome recessive type, Multiple epiphyseal dysplasia type 6 (EDM6) AR 9 6
COL9A2 Stickler syndrome, Multiple epiphyseal dysplasia type 2 (EDM2) AD/AR 7 12
COL9A3 Multiple epihyseal dysplasia type 3 (EDM3) AD/AR 10 14
CRYM Deafness AD 2 4
DCAF17 Woodhouse-Sakati syndrome AR 14 14
DCDC2 Deafness, Nephronophthisis, Sclerosing cholangitis, neonatal AR 13 9
DFNA5 Deafness AD 7 13
DFNB31 Deafness, Usher syndrome, type IV AR 12 31
DFNB59 Deafness AR 12 20
DIABLO Deafness AD 1 2
DIAPH1 Deafness, Seizures, cortical blindness, and microcephaly syndrome (SCBMS) AD/AR 10 15
DIAPH3 Non-syndromic sensorineural deafness AD 1 9
DLX5 Split-hand/foot malformation with sensorineural hearing loss AR 3 9
DMXL2 Deafness, autosomal dominant, 71 AR 2 6
DNMT1 Neuropathy, hereditary sensory, Cerebellar ataxia, deafness, and narcolepsy AD 9 20
DSPP Dentin dysplasia, Dentinogenesis imperfecta, Deafness, with dentinogenesis imperfecta AD 11 53
EDN3 Hirschsprung disease, Central hypoventilation syndrome, congenital, Waardenburg syndrome AD/AR 7 21
EDNRB Hirschsprung disease, ABCD syndrome, Waardenburg syndrome AD/AR 12 66
EIF3F Intellectual disability AR
ELMOD3 Deafness AR 1 2
EPS8 Deafness AR 2 2
EPS8L2 Deafness, autosomal recessive 106 AR 2 2
ESPN* Deafness, Usher syndrome, type IV AD/AR 12 15
ESRRB Deafness AR 12 19
EYA1 Otofaciocervical syndrome, Branchiootic syndrome, Branchiootorenal syndrome AD 56 218
EYA4 Dilated cardiomyopathy (DCM), Deafness, autosomal dominant 10 AD 15 28
FAM136A* Sensorineural hearing loss AD 1 2
FAM65B Deafness AR 1 2
FDXR Auditory neuropathy and optic atrophy AR 5 19
FGF3 Deafness, congenital with inner ear agenesis, microtia, and microdontia AR 13 20
FGFR3 Lacrimoauriculodentodigital syndrome, Muenke syndrome, Crouzon syndrome with acanthosis nigricans, Camptodactyly, tall stature, and hearing loss (CATSHL) syndrome, Achondroplasia, Hypochondroplasia, Thanatophoric dysplasia type 1, Thanatophoric dysplasia type 2, SADDAN AD/AR 54 77
FITM2 Dystonia, Deafness AR 1
FOXI1 Pendred syndrome, Enlarged vestibular aqueduct AR 1 11
GATA3 Hypomagnesemia, renal AD 22 86
GIPC3 Deafness AR 9 20
GJA1* Oculodentodigital dysplasia mild type, Oculodentodigital dysplasia severe type, Syndactyly type 3 AD/AR 31 107
GJB2 Deafness, Bart-Pumphrey syndrome, Keratoderma, palmoplantar, with deafness, Vohwinkel syndrome, Hystrix-like ichthyosis with deafness, Keratitis-icthyosis-deafness syndrome AD/AR/Digenic 133 405
GJB3 Deafness, Erythrokeratodermia variabilis et progressiva 1, Deafness, autosomal dominant 2B AD/AR 11 40
GJB6 Deafness, Deafness, autosomal dominant 3B, Ectodermal dysplasia, hidrotic (Clouston syndrome) AD/AR 10 33
GPSM2 Deafness, Chudley-McCullough syndrome AR 18 11
GRHL2 Ectodermal dysplasia/short stature syndrome, Deafness, autosomal dominant 28, Corneal dystrophy, posterior polymorphous AD/AR 12 12
GRXCR1 Deafness AR 8 9
GRXCR2 Deafness AR 1 2
HARS Usher syndrome, type IV, Charcot-Marie-Tooth disease, axonal, type 2W AR 6 12
HARS2 Perrault syndrome AR 7 3
HGF Deafness AR 4 10
HOMER2 Deafness AD 2 1
HOXB1 Facial paresis, hereditary congenital AR 3 6
HSD17B4 Perrault syndrome, D-bifunctional protein deficiency AR 60 99
ILDR1 Deafness AR 8 27
KARS Charcot-Marie-Tooth disease AR 9 23
KCNE1 Long QT syndrome, Jervell and Lange-Nielsen syndrome AD/AR/Digenic 11 46
KCNJ10 Seizures, sensorineural deafness, ataxia, mental retardation, and electrolyte imbalance (SESAME syndrome), Pendred syndrome, Enlarged vestibular aqueduct AR/Digenic 13 29
KCNQ1 Short QT syndrome, Long QT syndrome, Atrial fibrillation, Jervell and Lange-Nielsen syndrome AD/AR/Digenic 298 631
KCNQ4 Deafness AD 28 37
KIT Gastrointestinal stromal tumor, Piebaldism AD 79 116
LARS2 Perrault syndrome, Hydrops, lactic acidosis, and sideroblastic anemia (HLASA) AR 14 14
LHFPL5 Deafness AR 7 10
LMX1A Hearing loss AD/AR 1 4
LOXHD1 Deafness AD/AR 26 60
LRP2 Donnai-Barrow syndrome, Faciooculoacousticorenal syndrome AR 24 38
LRTOMT Deafness AR 7 17
MAN2B1 Mannosidosis, alpha B, lysosomal AR 63 149
MANBA Mannosidosis, lysosomal AR 16 19
MARVELD2 Deafness AR 9 17
MET Deafness, Renal cell carcinoma, papillary, Osteofibrous dysplasia, susceptibility to AD/AR 20 34
MGP Keutel syndrome AR 5 8
MIR96 Deafness AD 2 4
MITF Tietz albinism-deafness syndrome, Waardenburg syndrome, Coloboma, osteopetrosis, microphthalmia, macrocephaly, albinism, and deafness (COMMAD) AD/AR 32 58
MPZL2 Sensorineural hearing loss AR 4
MSRB3 Deafness AR 5 2
MYH14 Deafness, Peripheral neuropathy, myopathy, hoarseness, and hearing loss AD 7 44
MYH9 Sebastian syndrome, May-Hegglin anomaly, Epstein syndrome, Fechtner syndrome, Macrothrombocytopenia and progressive sensorineural deafness, Deafness, autosomal dominant 17 AD 25 117
MYO15A Deafness AR 97 235
MYO3A Deafness AR 9 22
MYO6 Deafness, Deafness, autosomal dominant, 22 AD/AR 24 68
MYO7A Deafness, Usher syndrome, type IV, Deafness, autosomal dominant 11 AD/AR 239 515
NARS2 Combined oxidative phosphorylation deficiency AR 12 12
NDP Exudative vitreoretinopathy, Norrie disease XL 31 167
NLRP3 Neonatal onset multisystem inflammatory disease (NOMID), Muckle-Wells syndrome, Chronic infantile neurologic cutaneous articular (CINCA) syndrome, Familial cold-induced autoinflammatory syndrome 1 AD 20 136
OSBPL2 Deafness AD 2 3
OTOA#* Deafness AR 19 28
OTOF Neuropathy, Deafness AR 107 163
OTOG Deafness AR 18 3
OTOGL Deafness AR 26 23
P2RX2 Deafness AD 2 4
PAX3 Craniofacial-deafness-hand syndrome, Waardenburg syndrome AD/AR 54 149
PCDH15 Deafness, Usher syndrome, type IV AR/Digenic 113 118
PDE1C Hearing loss AD 2 2
PDZD7# Usher syndrome, type IV, Deafness, autosomal recessive AR 11 19
PEX1 Heimler syndrome, Peroxisome biogenesis factor disorder 1A, Peroxisome biogenesis factor disorder 1B AR 112 134
PEX26 Adrenoleukodystrophy, neonatal, Zellweger syndrome, Peroxisome biogenesis disorder AR 13 27
PEX6 Heimler syndrome, Peroxisome biogenesis disorder 4A, Peroxisome biogenesis disorder 4B AR 58 107
PISD AR
PNPT1* Deafness, Combined oxidative phosphorylation deficiency, 13 AR 11 13
POLR1C# Treacher Collins syndrome AR 17 21
POLR1D Treacher Collins syndrome AD/AR 9 26
POU3F4 Deafness XL 25 80
POU4F3 Deafness AD 9 33
PRPS1* Phosphoribosylpyrophosphate synthetase I superactivity, Arts syndrome, Charcot-Marie-Tooth disease, X-linked recessive, 5, Deafness, X-linked 1 XL 27 32
RDX* Deafness AR 6 10
RMND1* Combined oxidative phosphorylation deficiency AR 17 15
RPS6KA3 Coffin-Lowry syndrome, Mental retardation XL 65 171
S1PR2 Deafness, autosomal recessive 68 AR 2 3
SALL1* Townes-Brocks syndrome 1 AD 31 87
SALL4 Acro-renal-ocular syndrome, Duane-radial ray/Okohiro syndrome AD 21 56
SEMA3E CHARGE syndrome AD 1 4
SERPINB6 Deafness AR 2 3
SIX1 Deafness, Branchiootic syndrome, Branchiootorenal syndrome AD 11 19
SIX5 Branchiootorenal syndrome AD 3 10
SLC17A8 Deafness AD 1 8
SLC19A2 Thiamine-responsive megaloblastic anemia syndrome AR 14 51
SLC22A4 Hearing loss AR 2
SLC26A4 Deafness, Pendred syndrome, Enlarged vestibular aqueduct AR 181 548
SLC26A5 Deafness AR 2 7
SLC29A3 Histiocytosis-lymphadenopathy plus syndrome, Dysosteosclerosis AR 17 25
SLC33A1* Congenital cataracts, hearing loss, and neurodegeneration, Spastic paraplegia 42, autosomal dominant AD/AR 6 7
SLC52A2 Brown-Vialetto-Van Laere syndrome AR 27 25
SLC52A3 Fazio-Londe disease, Brown-Vialetto-Van Laere syndrome AR 30 42
SLITRK6 Deafness and myopia AR 3 5
SMAD4 Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome, Polyposis, juvenile intestinal, Myhre dysplasia, Hereditary hemorrhagic telangiectasia AD 179 143
SMPX Deafness XL 8 14
SNAI2 Waardenburg syndrome, Piebaldism AR 2 4
SOX10 Peripheral demyelinating neuropathy, central dysmyelination, Waardenburg syndrome, and Hirschsprung disease, Kallmann syndrome AD 56 148
SPATA5 Schizophrenia, Epilepsy, hearing loss, and mental retardation syndrome (EHLMRS) AR 27 27
STAG2 Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder XL 6 14
STRC#* Deafness AR 31 85
SUCLA2 Mitochondrial DNA depletion syndrome AR 9 29
SUCLG1 Mitochondrial DNA depletion syndrome AR 12 28
SYNE4 Deafness AR 6 2
SYT2* Myasthenic syndrome, congenital 7, presynaptic AD 3 3
TBC1D24 Deafness, onychodystrophy, osteodystrophy, mental retardation, and seizures (DOORS) syndrome, Deafness, autosomal dominant, 65, Myoclonic epilepsy, infantile, familial, Epileptic encephalopathy, early infantile, 16, Deafness, autosomal recessive 86 AD/AR 43 55
TBL1X Congenital hypothyroidism, Hearing loss 2 8
TCOF1 Treacher Collins syndrome AD 50 330
TECTA Deafness AD/AR 36 120
TFAP2A Branchiooculofacial sydrome AD 23 42
TIMM8A* Mohr-Tranebjaerg syndrome, Jensen syndrome, Opticoacoustic nerve atrophy with dementia XL 11 21
TJP2 Cholestasis, progressive familial intrahepatic, Hypercholanemia, familial, Deafness, autosomal dominant 51 AD/AR 25 27
TMC1 Deafness, Deafness, autosomal dominant 36 AD/AR 33 91
TMEM132E Hearing loss AR 1
TMIE Deafness AR 9 10
TMPRSS3 Deafness AR 25 82
TNC Deafness AD 3 6
TPRN# Deafness AR 6 12
TRIOBP Deafness AR 22 40
TRMU Liver failure, infantile, Reversible infantile respiratory chain deficiency AR 20 21
TSHZ1 Aural atresia, congenital AD 2 4
TSPEAR Deafness AR 2 7
TUBB4B Leber congenital amaurosis, Hearing loss AD 2 3
TYR* Albinism, oculocutaneous AR 77 441
USH1C Deafness, Usher syndrome, type IV AR 45 51
USH1G Usher syndrome, type IV AR 13 32
USH2A Retinitis pigmentosa 39, Usher syndrome, type 2A AR 401 1169
VCAN Wagner disease AD 11 19
WBP2 Deafness, autosomal recessive 107 AR 3 3
WFS1 Wolfram syndrome, Deafness, Wolfram-like syndrome, autosomal dominant, Deafness, autosomal dominant 6/14/38, Cataract 41 AD/AR 69 362
XYLT2 Primrose syndrome AR 2 10

* Some, or all, of the gene is duplicated in the genome. Read more.

# The gene has suboptimal coverage (means <90% of the gene’s target nucleotides are covered at >20x with mapping quality score (MQ>20) reads), and/or the gene has exons listed under Test limitations section that are not included in the panel as they are not sufficiently covered with high quality sequence reads.

The sensitivity to detect variants may be limited in genes marked with an asterisk (*) or number sign (#)

Gene refers to the HGNC approved gene symbol; Inheritance refers to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR), X-linked (XL), X-linked dominant (XLD) and X-linked recessive (XLR); ClinVar refers to the number of variants in the gene classified as pathogenic or likely pathogenic in this database (ClinVar); HGMD refers to the number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD). The list of associated, gene specific phenotypes are generated from CGD or Orphanet databases.

Non-coding variants covered by Comprehensive Hearing Loss and Deafness Panel

Gene Genomic location HG19 HGVS RefSeq RS-number
AIFM1 ChrX:129274636 c.697-44T>G NM_004208.3
ANKH Chr5:14871567 c.-11C>T NM_054027.4
BCS1L Chr2:219524871 c.-147A>G NM_004328.4
BCS1L Chr2:219525123 c.-50+155T>A NM_004328.4 rs386833855
BTD Chr3:15683399 c.310-15delT NM_000060.2 rs587783008
BTD Chr3:15687154 c.*159G>A NM_000060.2 rs530872564
CDKN1C Chr11:2905209 c.*5+20G>T NM_000076.2 rs760540648
CHD7 Chr8:61734568 c.2836-15C>G NM_017780.3
CHD7 Chr8:61757794 c.5051-15T>A NM_017780.3
CHD7 Chr8:61763034 c.5405-18C>A NM_017780.3 rs199981784
CHD7 Chr8:61763035 c.5405-17G>A NM_017780.3 rs794727423
CHD7 Chr8:61763039 c.5405-13G>A NM_017780.3 rs1131690787
CLRN1 Chr3:150660197 c.254-649T>G NM_001195794.1 rs976853535
COL11A1 Chr1:103386637 c.3744+437T>G NM_080629.2
COL11A1 Chr1:103488576 c.1027-24A>G NM_080629.2
COL11A1 Chr1:103491958 c.781-450T>G NM_080629.2 rs587782990
COL2A1 Chr12:48379984 c.1527+135G>A NM_001844.4
COL4A3 Chr2:228145145 c.2224-11C>T NM_000091.4
COL4A3 Chr2:228168708 c.4028-27A>G NM_000091.4
COL4A3 Chr2:228173092 c.4462+457C>G NM_000091.4
COL4A3 Chr2:228173596 c.4463-18dupA NM_000091.4 rs769590145
COL4A4 Chr2:227875240 c.4334-23A>G NM_000092.4
COL4A5 ChrX:107813924 c.385-719G>A NM_033380.2 rs104886396
COL4A5 ChrX:107816792 c.466-12G>A NM_033380.2 rs104886414
COL4A5 ChrX:107820077 c.609+875G>T NM_033380.2
COL4A5 ChrX:107821295 c.646-12_646-11delTT NM_033380.2 rs104886436
COL4A5 ChrX:107834930 c.1423+57dupC NM_033380.2 rs104886328
COL4A5 ChrX:107838719 c.1424-20T>A NM_033380.2 rs281874668
COL4A5 ChrX:107842994 c.1948+894C>G NM_033380.2
COL4A5 ChrX:107845097 c.2042-18A>G NM_033380.2
COL4A5 ChrX:107849932 c.2245-40A>G NM_033380.2
COL4A5 ChrX:107849958 c.2245-14T>A NM_033380.2
COL4A5 ChrX:107852872 c.2395+2750A>G NM_033380.2
COL4A5 ChrX:107908726 c.3374-11C>A NM_033380.2 rs104886387
COL4A5 ChrX:107933678 c.4529-2300T>G NM_033380.2
COL4A5 ChrX:107935633 c.4529-345A>G NM_033380.2
COL4A5 ChrX:107938272 c.4821+121T>C NM_033380.2 rs104886423
COL4A5 ChrX:107938337 c.4822-152dupT NM_033380.2
COL4A5 ChrX:107938346 c.4822-151_4822-150insT NM_033380.2 rs397515494
DCAF17 Chr2:172305176 c.322-14delC NM_025000.3 rs201494527
DFNA5 Chr7:24746007 c.991-15_991-13delTTC NM_004403.2 rs727505273
DIAPH3 Chr13:60738072 c.-172G>A NM_001042517.1
DIAPH3 Chr13:60738073 c.-173C>T NM_001042517.1
EDN3 Chr20:57875743 c.-125G>A NM_000114.2
EDN3 Chr20:57875849 c.-19C>A NM_000114.2 rs375594972
EYA1 Chr8:72156939 c.1051-12T>G NM_000503.4
EYA1 Chr8:72211483 c.640-15G>A NM_000503.4
EYA4 Chr6:133833847 c.1282-12T>A NM_004100.4
EYA4 Chr6:133833997 c.1341-19T>A NM_004100.4
GJB2 Chr13:20763744 c.-22-2A>C NM_004004.5 rs201895089
GJB2 Chr13:20766920 c.-23+2T>A NM_004004.5
GJB2 Chr13:20766921 c.-23+1G>A NM_004004.5 rs80338940
GJB2 Chr13:20766922 c.-23G>T NM_004004.5 rs786204734
GJB2 Chr13:20767158 c.-259C>T NM_004004.5
GJB2 Chr13:20767159 c.-260C>T NM_004004.5
GRHL2 Chr8:102505149 c.20+133delA NM_024915.3
GRHL2 Chr8:102505272 c.20+257delT NM_024915.3
GRHL2 Chr8:102505561 c.20+544G>T NM_024915.3
GRXCR1 Chr4:42965170 c.627+19A>T NM_001080476.2 rs201824235
HGF Chr7:81384504 c.482+1991_482+2000delGATGATGAAA NM_000601.4 rs900334407
HGF Chr7:81384516 c.482+1986_482+1988delTGA NM_000601.4
HSD17B4 Chr5:118837725 c.1285-11C>G NM_001199291.1 rs779466683
KCNJ10 Chr1:160039811 c.-1+1G>T NM_002241.4 rs796052606
KCNQ1 Chr11:2484803 c.386+18089T>C NM_000218.2
MYO3A Chr10:26409593 c.1777-12G>A NM_017433.4
MYO6 Chr6:76593963 c.2417-1758T>G NM_004999.3
MYO7A Chr11:76839534 c.-48A>G NM_000260.3
MYO7A Chr11:76893448 c.3109-21G>A NM_000260.3
MYO7A Chr11:76915107 c.5327-14T>G NM_000260.3
MYO7A Chr11:76915110 c.5327-11A>G NM_000260.3 rs397516316
MYO7A Chr11:76919448 c.5857-27_5857-26insTTGAG NM_000260.3
NDP ChrX:43818099 c.-207-1G>A NM_000266.3
NDP ChrX:43832545 c.-208+5G>A NM_000266.3
NDP ChrX:43832548 c.-208+2T>G NM_000266.3
NDP ChrX:43832549 c.-208+1G>A NM_000266.3
NDP ChrX:43832685 c.-343A>G NM_000266.3 rs895911086
NDP ChrX:43832722 c.-391_-380delCTCTCTCTCCCTinsGTCTCTC NM_000266.3
NDP ChrX:43832724 c.-396_-383delTCCCTCTCTCTCTC NM_000266.3 rs770996360
PAX3 Chr2:223085913 c.958+28A>T NM_181459.3
PCDH15 Chr10:56560684 c.-29+1G>C NM_001142763.1
PEX6 Chr6:42933858 c.2301-15C>G NM_000287.3 rs267608236
PEX6 Chr6:42933952 c.2300+28G>A NM_000287.3 rs267608237
RPS6KA3 ChrX:20191268 c.1228-279T>G NM_004586.2
RPS6KA3 ChrX:20213274 c.326-11A>G NM_004586.2
SLC26A4 Chr7:107301201 c.-103T>C NM_000441.1 rs60284988
SLC26A4 Chr7:107301244 c.-60A>G NM_000441.1 rs545973091
SLC26A4 Chr7:107301301 c.-4+1G>C NM_000441.1
SLC26A4 Chr7:107301305 c.-4+5G>A NM_000441.1 rs727503425
SLC26A4 Chr7:107323842 c.918+45_918+47delCAA NM_000441.1
SLC26A4 Chr7:107330533 c.1150-35_1150-28delTTTGTAGG NM_000441.1
SLC26A4 Chr7:107334836 c.1264-12T>A NM_000441.1
SLC26A4 Chr7:107336364 c.1438-7dupT NM_000441.1 rs754734032
SLC26A4 Chr7:107341513 c.1708-27_1708-11delTAAGTAACTTGACATTT NM_000441.1
SLC26A4 Chr7:107350439 c.2090-52_2090-49delCAAA NM_000441.1
SLC29A3 Chr10:73122778 c.*413G>A NM_018344.5
SLC52A2 Chr8:145582843 c.-110-1G>A NM_024531.4
SNAI2 Chr8:49833972 c.-149_-148delCGinsTA NM_003068.4
SOX10 Chr22:38379877 c.-84-2A>T NM_006941.3
SOX10 Chr22:38412215 c.-31954C>T NM_006941.3 rs606231342
SOX10 Chr22:38412781 c.-32520C>G NM_006941.3
TIMM8A ChrX:100601671 c.133-23A>C NM_004085.3 rs869320666
TMC1 Chr9:75315577 c.362+18A>G NM_138691.2
TYR Chr11:88960973 c.1037-18T>G NM_000372.4
USH2A Chr1:215821092 c.14583-20C>G NM_206933.2
USH2A Chr1:215967783 c.9959-4159A>G NM_206933.2
USH2A Chr1:216039721 c.8845+628C>T NM_206933.2
USH2A Chr1:216064540 c.7595-2144A>G NM_206933.2 rs786200928
USH2A Chr1:216247476 c.5573-834A>G NM_206933.2
USH2A Chr1:216592035 c.486-14G>A NM_206933.2 rs374536346
USH2A Chr1:216596610 c.-259G>T NM_206933.2
WFS1 Chr4:6271704 c.-43G>T NM_006005.3

Added and removed genes from the panel

Genes added Genes removed
ARSG
ATP2B2
CATSPER2
CDC42
CDK9
CEP250
DMXL2
EIF3F
FAM136A
FITM2
LMX1A
MPZL2
PDE1C
PISD
SLC22A4
STAG2
SYT2
TBL1X
TSHZ1
TUBB4B
XYLT2

Test Strengths

The strengths of this test include:
  • CAP accredited laboratory
  • CLIA-certified personnel performing clinical testing in a CLIA-certified laboratory
  • Powerful sequencing technologies, advanced target enrichment methods and precision bioinformatics pipelines ensure superior analytical performance
  • Careful construction of clinically effective and scientifically justified gene panels
  • Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level
  • Our publicly available analytic validation demonstrating complete details of test performance
  • ~2,000 non-coding disease causing variants in our clinical grade NGS assay for panels (please see ‘Non-coding disease causing variants covered by this panel’ in the Panel Content section)
  • Our rigorous variant classification scheme
  • Our systematic clinical interpretation workflow using proprietary software enabling accurate and traceable processing of NGS data
  • Our comprehensive clinical statements

Test Limitations

Variants in the KCNE1 gene should not be used for risk assessment at the moment. Specifically, KCNE1 c.253G>A, p.(Asp85Asn) variant has been considered to be a mild risk factor for acquired long QT syndrome. However, in the newest version of the reference genome GRCh38, a gene KCNE1B, nearly identical to KCNE1 has appeared. By using standard NGS technologies, as well as Sanger sequencing, it is not possible to get reliable region-specific sequences for these genes. It is likely that reads that have been earlier mapped to KCNE1 actually belong to KCNE1B. Moreover, it is currently unclear whether KCNE1B produces a protein product, and if a protein is produced, whether the gene is expressed in heart. More independent data characterizing KCNE1B and its function are needed. Currently, all KCNE1 sequence data and the literature related to KCNE1 variants should be interpreted with caution. The following exons are not included in the panel as they are not sufficiently covered with high quality sequence reads: OTOA (NM_144672:22-27), PDZD7 (NM_024895:10), POLR1C (NM_001318876:9), STRC (NM_153700:1-18). Genes with suboptimal coverage in our assay are marked with number sign (#) and genes with partial, or whole gene, segmental duplications in the human genome are marked with an asterisk (*) if they overlap with the UCSC pseudogene regions. Gene is considered to have suboptimal coverage when >90% of the gene’s target nucleotides are not covered at >20x with mapping quality score (MQ>20) reads. The technology may have limited sensitivity to detect variants in genes marked with these symbols (please see the Panel content table above).

This test does not detect the following:
  • Complex inversions
  • Gene conversions
  • Balanced translocations
  • Mitochondrial DNA variants
  • Repeat expansion disorders unless specifically mentioned
  • Non-coding variants deeper than ±20 base pairs from exon-intron boundary unless otherwise indicated (please see above Panel Content / non-coding variants covered by the panel).
This test may not reliably detect the following:
  • Low level mosaicism (variant with a minor allele fraction of 14.6% is detected with 90% probability)
  • Stretches of mononucleotide repeats
  • Indels larger than 50bp
  • Single exon deletions or duplications
  • Variants within pseudogene regions/duplicated segments

The sensitivity of this test may be reduced if DNA is extracted by a laboratory other than Blueprint Genetics.

For additional information, please refer to the Test performance section and see our Analytic Validation.

The genes on the panel have been carefully selected based on scientific literature, mutation databases and our experience.

Our panels are sectioned from our high-quality, clinical grade NGS assay. Please see our sequencing and detection performance table for details regarding our ability to detect different types of alterations (Table).

Assays have been validated for various sample types including EDTA-blood, isolated DNA (excluding from formalin fixed paraffin embedded tissue), saliva and dry blood spots (filter cards). These sample types were selected in order to maximize the likelihood for high-quality DNA yield. The diagnostic yield varies depending on the assay used, referring healthcare professional, hospital and country. Plus analysis increases the likelihood of finding a genetic diagnosis for your patient, as large deletions and duplications cannot be detected using sequence analysis alone. Blueprint Genetics’ Plus Analysis is a combination of both sequencing and deletion/duplication (copy number variant (CNV)) analysis.

Performance of Blueprint Genetics high-quality, clinical grade NGS sequencing assay for panels.

Sensitivity % (TP/(TP+FN) Specificity %
Single nucleotide variants 99.89% (99,153/99,266) >99.9999%
Insertions, deletions and indels by sequence analysis
1-10 bps 96.9% (7,563/7,806) >99.9999%
11-50 bps 99.13% (2,524/2,546) >99.9999%
Copy number variants (exon level dels/dups)
1 exon level deletion (heterozygous) 100% (20/20) NA
1 exon level deletion (homozygous) 100% (5/5) NA
1 exon level deletion (het or homo) 100% (25/25) NA
2-7 exon level deletion (het or homo) 100% (44/44) NA
1-9 exon level duplication (het or homo) 75% (6/8) NA
Simulated CNV detection
5 exons level deletion/duplication 98.7% 100.00%
Microdeletion/-duplication sdrs (large CNVs, n=37))
Size range (0.1-47 Mb) 100% (37/37)
     
The performance presented above reached by Blueprint Genetics high-quality, clinical grade NGS sequencing assay with the following coverage metrics
     
Mean sequencing depth 143X
Nucleotides with >20x sequencing coverage (%) 99.86%

Bioinformatics

The target region for each gene includes coding exons and ±20 base pairs from the exon-intron boundary. In addition, the panel includes non-coding and regulatory variants if listed above (Non-coding variants covered by the panel). Some regions of the gene(s) may be removed from the panel if specifically mentioned in the ‘Test limitations” section above. The sequencing data generated in our laboratory is analyzed with our proprietary data analysis and annotation pipeline, integrating state-of-the art algorithms and industry-standard software solutions. Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results. Our pipeline is streamlined to maximize sensitivity without sacrificing specificity. We have incorporated a number of reference population databases and mutation databases including, but not limited, to 1000 Genomes Project, gnomAD, ClinVar and HGMD into our clinical interpretation software to make the process effective and efficient. For missense variants, in silico variant prediction tools such as  SIFT, PolyPhen, MutationTaster are used to assist with variant classification. Through our online ordering and statement reporting system, Nucleus, ordering providers have access to the details of the analysis, including patient specific sequencing metrics, a gene level coverage plot and a list of regions with <20X sequencing depth if applicable. This reflects our mission to build fully transparent diagnostics where ordering providers can easily visualize the crucial details of the analysis process.

Clinical interpretation

We provide customers with the most comprehensive clinical report available on the market. Clinical interpretation requires a fundamental understanding of clinical genetics and genetic principles. At Blueprint Genetics, our PhD molecular geneticists, medical geneticists and clinical consultants prepare the clinical statement together by evaluating the identified variants in the context of the phenotypic information provided in the requisition form. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals regardless of whether they have formal training in genetics.

Variant classification is the corner stone of clinical interpretation and resulting patient management decisions. Our classifications follow the Blueprint Genetics Variant Classification Schemes based on the ACMG guideline 2015. Minor modifications were made to increase reproducibility of the variant classification and improve the clinical validity of the report. Our experience with tens of thousands of clinical cases analyzed at our laboratory allowed us to further develop the industry standard.

The final step in the analysis is orthogonal confirmation. Sequence variants classified as pathogenic, likely pathogenic and variants of uncertain significance (VUS) are confirmed using bi-directional Sanger sequencing when they do not meet our stringent NGS quality metrics for a true positive call.
Reported heterozygous and homo/hemizygous copy number variations with a size <10 and <3 target exons are confirmed by orthogonal methods such as qPCR if the specific CNV has been seen and confirmed less than three times at Blueprint Genetics.

Our clinical statement includes tables for sequencing and copy number variants that include basic variant information (genomic coordinates, HGVS nomenclature, zygosity, allele frequencies, in silico predictions, OMIM phenotypes and classification of the variant). In addition, the statement includes detailed descriptions of the variant, gene and phenotype(s) including the role of the specific gene in human disease, the mutation profile, information about the gene’s variation in population cohorts and detailed information about related phenotypes. We also provide links to the references, abstracts and variant databases used to help ordering providers further evaluate the reported findings if desired. The conclusion summarizes all of the existing information and provides our rationale for the classification of the variant.

Identification of pathogenic or likely pathogenic variants in dominant disorders or their combinations in different alleles in recessive disorders are considered molecular confirmation of the clinical diagnosis. In these cases, family member testing can be used for risk stratification. We do not recommend using variants of uncertain significance (VUS) for family member risk stratification or patient management. Genetic counseling is recommended.

Our interpretation team analyzes millions of variants from thousands of individuals with rare diseases. Our internal database and our understanding of variants and related phenotypes increases with every case analyzed. Our laboratory is therefore well-positioned to re-classify previously reported variants as new information becomes available. If a variant previously reported by Blueprint Genetics is re-classified, our laboratory will issue a follow-up statement to the original ordering health care provider at no additional cost.

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